Biological responses to light from the environment involve protein-chromophore partnerships that act in damage avoidance, DMA damage repair, and transcriptional regulation. This research aims to understand the structural biochemistry underlying these chromatically active protein responses, including the mechanisms by which a) the protein environment tunes the spectral properties of chromophores, and b) light absorption by the chromophore is transduced to protein conformational changes and biological activities. To address the challenge of understanding the specific molecular mechanisms producing these biological responses to light, we propose focused, interdisciplinary characterizations of two major families of inter-related chromatically-active proteins: 1) the PAS domain family typified by the light-cycling bacterial photoreceptor photoactive yellow protein (PYP), which acts in blue-light damage avoidance, plus circadian clock proteins that contain PAS domains for which PYP is the prototype;and 2) the photolyase (PHR) and cryptochrome (CRY) family of light-activated, redox-active, flavin-containing enzymes and their PAS domain protein partners. Together, these photoactive protein families will allow detailed and comparative analyses of the fundamental molecular properties underlying the synergistic interactions of chromophores, proteins, and partners. Our overall project goal is to understand how nature applies these fundamental properties to promote and regulate functionally important conformational changes and interactions that mediate photoactive protein signal transduction and biological functions. We will correlate protein structural and spectroscopic states by integrating spectroscopic and high-resolution X-ray crystallographic results with mutagenesis, biochemical assays, and hydrogen-deuterium exchange mass spectrometry (DXMS). Our results will provide a framework for identifying and testing underlying mechanistic principles for key families of protein-chromophore partnerships, along with their associated functionally-important conformational changes and intermolecular interactions.